{"id":"https://openalex.org/W4412454128","doi":"https://doi.org/10.1093/bioinformatics/btaf230","title":"Predicting coarse-grained representations of biogeochemical cycles from metabarcoding data","display_name":"Predicting coarse-grained representations of biogeochemical cycles from metabarcoding data","publication_year":2025,"publication_date":"2025-04-28","ids":{"openalex":"https://openalex.org/W4412454128","doi":"https://doi.org/10.1093/bioinformatics/btaf230","pmid":"https://pubmed.ncbi.nlm.nih.gov/40662816"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf230","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf230","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i49/63745560/btaf230.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i49/63745560/btaf230.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052921070","display_name":"Arnaud Belcour","orcid":"https://orcid.org/0000-0003-1170-0785"},"institutions":[{"id":"https://openalex.org/I106785703","display_name":"Institut polytechnique de Grenoble","ror":"https://ror.org/05sbt2524","country_code":"FR","type":"education","lineage":["https://openalex.org/I106785703","https://openalex.org/I899635006"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210101348","display_name":"Centre Inria de l'Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/00n8d6z93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210101348"]},{"id":"https://openalex.org/I899635006","display_name":"Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/02rx3b187","country_code":"FR","type":"education","lineage":["https://openalex.org/I899635006"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Arnaud Belcour","raw_affiliation_strings":["Univ. Grenoble Alpes, Inria , 38000 Grenoble,","Universit\u00e9 Grenoble Alpes, CNRS, LIPhy , 38000 Grenoble,"],"raw_orcid":"https://orcid.org/0000-0003-1170-0785","affiliations":[{"raw_affiliation_string":"Univ. Grenoble Alpes, Inria , 38000 Grenoble,","institution_ids":["https://openalex.org/I4210101348","https://openalex.org/I899635006","https://openalex.org/I106785703"]},{"raw_affiliation_string":"Universit\u00e9 Grenoble Alpes, CNRS, LIPhy , 38000 Grenoble,","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I899635006"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5116113627","display_name":"Loris Megy","orcid":null},"institutions":[{"id":"https://openalex.org/I106785703","display_name":"Institut polytechnique de Grenoble","ror":"https://ror.org/05sbt2524","country_code":"FR","type":"education","lineage":["https://openalex.org/I106785703","https://openalex.org/I899635006"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210101348","display_name":"Centre Inria de l'Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/00n8d6z93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210101348"]},{"id":"https://openalex.org/I899635006","display_name":"Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/02rx3b187","country_code":"FR","type":"education","lineage":["https://openalex.org/I899635006"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Loris Megy","raw_affiliation_strings":["Gricad, Inria, CNRS, Universit\u00e9 Grenoble Alpes, Grenoble INP , 38000 Grenoble,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Gricad, Inria, CNRS, Universit\u00e9 Grenoble Alpes, Grenoble INP , 38000 Grenoble,","institution_ids":["https://openalex.org/I4210101348","https://openalex.org/I1294671590","https://openalex.org/I899635006","https://openalex.org/I106785703"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073507144","display_name":"Sylvain St\u00e9phant","orcid":"https://orcid.org/0000-0002-3213-2054"},"institutions":[{"id":"https://openalex.org/I1286329397","display_name":"United States Geological Survey","ror":"https://ror.org/035a68863","country_code":"US","type":"government","lineage":["https://openalex.org/I1286329397","https://openalex.org/I1335927249"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sylvain Stephant","raw_affiliation_strings":["French Geological Survey (BRGM) , 45060 Orl\u00e9ans,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"French Geological Survey (BRGM) , 45060 Orl\u00e9ans,","institution_ids":["https://openalex.org/I1286329397"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047180160","display_name":"Caroline Michel","orcid":"https://orcid.org/0000-0002-0515-4637"},"institutions":[{"id":"https://openalex.org/I1286329397","display_name":"United States Geological Survey","ror":"https://ror.org/035a68863","country_code":"US","type":"government","lineage":["https://openalex.org/I1286329397","https://openalex.org/I1335927249"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Caroline Michel","raw_affiliation_strings":["French Geological Survey (BRGM) , 45060 Orl\u00e9ans,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"French Geological Survey (BRGM) , 45060 Orl\u00e9ans,","institution_ids":["https://openalex.org/I1286329397"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019409044","display_name":"S\u00e9tareh Rad","orcid":"https://orcid.org/0000-0003-0703-7327"},"institutions":[{"id":"https://openalex.org/I1286329397","display_name":"United States Geological Survey","ror":"https://ror.org/035a68863","country_code":"US","type":"government","lineage":["https://openalex.org/I1286329397","https://openalex.org/I1335927249"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S\u00e9tareh Rad","raw_affiliation_strings":["French Geological Survey (BRGM) , 45060 Orl\u00e9ans,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"French Geological Survey (BRGM) , 45060 Orl\u00e9ans,","institution_ids":["https://openalex.org/I1286329397"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020496561","display_name":"Petra Bombach","orcid":null},"institutions":[{"id":"https://openalex.org/I4210101269","display_name":"Institut f\u00fcr Stahlbau Leipzig (Germany)","ror":"https://ror.org/015706c71","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210101269"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Petra Bombach","raw_affiliation_strings":["Isodetect GmbH , 04103 Leipzig,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Isodetect GmbH , 04103 Leipzig,","institution_ids":["https://openalex.org/I4210101269"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039491109","display_name":"Nicole Dopffel","orcid":"https://orcid.org/0000-0003-0020-9579"},"institutions":[{"id":"https://openalex.org/I4210107808","display_name":"NORCE Research AS","ror":"https://ror.org/02gagpf75","country_code":"NO","type":"facility","lineage":["https://openalex.org/I4210107808"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Nicole Dopffel","raw_affiliation_strings":["NORCE Norwegian Research Center AS , 5008 Bergen,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NORCE Norwegian Research Center AS , 5008 Bergen,","institution_ids":["https://openalex.org/I4210107808"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054406248","display_name":"Hidde de Jong","orcid":"https://orcid.org/0000-0002-2226-650X"},"institutions":[{"id":"https://openalex.org/I106785703","display_name":"Institut polytechnique de Grenoble","ror":"https://ror.org/05sbt2524","country_code":"FR","type":"education","lineage":["https://openalex.org/I106785703","https://openalex.org/I899635006"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210101348","display_name":"Centre Inria de l'Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/00n8d6z93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210101348"]},{"id":"https://openalex.org/I899635006","display_name":"Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/02rx3b187","country_code":"FR","type":"education","lineage":["https://openalex.org/I899635006"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Hidde de Jong","raw_affiliation_strings":["Univ. Grenoble Alpes, Inria , 38000 Grenoble,","Universit\u00e9 Grenoble Alpes, CNRS, LIPhy , 38000 Grenoble,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Univ. Grenoble Alpes, Inria , 38000 Grenoble,","institution_ids":["https://openalex.org/I4210101348","https://openalex.org/I899635006","https://openalex.org/I106785703"]},{"raw_affiliation_string":"Universit\u00e9 Grenoble Alpes, CNRS, LIPhy , 38000 Grenoble,","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I899635006"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062022864","display_name":"Delphine Ropers","orcid":"https://orcid.org/0000-0003-2659-3003"},"institutions":[{"id":"https://openalex.org/I106785703","display_name":"Institut polytechnique de Grenoble","ror":"https://ror.org/05sbt2524","country_code":"FR","type":"education","lineage":["https://openalex.org/I106785703","https://openalex.org/I899635006"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210101348","display_name":"Centre Inria de l'Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/00n8d6z93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210101348"]},{"id":"https://openalex.org/I899635006","display_name":"Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/02rx3b187","country_code":"FR","type":"education","lineage":["https://openalex.org/I899635006"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Delphine Ropers","raw_affiliation_strings":["Univ. Grenoble Alpes, Inria , 38000 Grenoble,","Universit\u00e9 Grenoble Alpes, CNRS, LIPhy , 38000 Grenoble,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Univ. Grenoble Alpes, Inria , 38000 Grenoble,","institution_ids":["https://openalex.org/I4210101348","https://openalex.org/I899635006","https://openalex.org/I106785703"]},{"raw_affiliation_string":"Universit\u00e9 Grenoble Alpes, CNRS, LIPhy , 38000 Grenoble,","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I899635006"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":9,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.3607,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.87919967,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"41","issue":"Supplement_1","first_page":"i49","last_page":"i57"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.5878000259399414,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.5878000259399414,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.12250000238418579,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12640","display_name":"Environmental DNA in Biodiversity Studies","score":0.11029999703168869,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biogeochemical-cycle","display_name":"Biogeochemical cycle","score":0.8563779592514038},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.7515403032302856},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7152958512306213},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6457945108413696},{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.557921290397644},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5056555271148682},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3594565987586975},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.2648404836654663},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19538423418998718},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.091716468334198}],"concepts":[{"id":"https://openalex.org/C71915725","wikidata":"https://www.wikidata.org/wiki/Q846303","display_name":"Biogeochemical cycle","level":2,"score":0.8563779592514038},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.7515403032302856},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7152958512306213},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6457945108413696},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.557921290397644},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5056555271148682},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3594565987586975},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.2648404836654663},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19538423418998718},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.091716468334198},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058893","descriptor_name":"DNA Barcoding, Taxonomic","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058893","descriptor_name":"DNA Barcoding, Taxonomic","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058893","descriptor_name":"DNA Barcoding, Taxonomic","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058893","descriptor_name":"DNA Barcoding, Taxonomic","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaf230","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf230","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i49/63745560/btaf230.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40662816","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40662816","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:HAL:hal-04938367v2","is_oa":true,"landing_page_url":"https://inria.hal.science/hal-04938367","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2025, 41 (Supplement_1), pp.i49-i57. &#x27E8;10.1093/bioinformatics/btaf230&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:pubmedcentral.nih.gov:12261419","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12261419","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf230","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf230","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i49/63745560/btaf230.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1157397619","display_name":null,"funder_award_id":"ANR-23-CETP-0002","funder_id":"https://openalex.org/F7400742617","funder_display_name":"Vermont Agency of Natural Resources"},{"id":"https://openalex.org/G1230417650","display_name":null,"funder_award_id":"GA N\u00b0101069750","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6757627240","display_name":null,"funder_award_id":"ANR-23-CETP-0002","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G7213322247","display_name":null,"funder_award_id":"101069750","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F7400742617","display_name":"Vermont Agency of Natural Resources","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412454128.pdf","grobid_xml":"https://content.openalex.org/works/W4412454128.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W183117647","https://openalex.org/W1975522326","https://openalex.org/W2011301426","https://openalex.org/W2034285706","https://openalex.org/W2063763762","https://openalex.org/W2098290178","https://openalex.org/W2099817249","https://openalex.org/W2130517250","https://openalex.org/W2138122982","https://openalex.org/W2142678478","https://openalex.org/W2149415648","https://openalex.org/W2229420368","https://openalex.org/W2277953252","https://openalex.org/W2295190630","https://openalex.org/W2513506562","https://openalex.org/W2605897695","https://openalex.org/W2766358903","https://openalex.org/W2774551105","https://openalex.org/W2899906720","https://openalex.org/W2900629010","https://openalex.org/W2950954328","https://openalex.org/W2996558561","https://openalex.org/W3024376490","https://openalex.org/W3025757981","https://openalex.org/W3030441098","https://openalex.org/W3031621681","https://openalex.org/W3120344562","https://openalex.org/W3150635270","https://openalex.org/W3182084436","https://openalex.org/W3194532145","https://openalex.org/W3203343200","https://openalex.org/W4214637392","https://openalex.org/W4220951604","https://openalex.org/W4221070127","https://openalex.org/W4280520289","https://openalex.org/W4307268214","https://openalex.org/W4310157184","https://openalex.org/W4366352204","https://openalex.org/W4392284791","https://openalex.org/W4398182689","https://openalex.org/W4399513068","https://openalex.org/W4399538195","https://openalex.org/W4400006710","https://openalex.org/W4403442555","https://openalex.org/W4403686464","https://openalex.org/W4404458588","https://openalex.org/W4404468965","https://openalex.org/W4411392672","https://openalex.org/W6607451195","https://openalex.org/W6771930094","https://openalex.org/W6859020953","https://openalex.org/W6930709533","https://openalex.org/W6930804618"],"related_works":["https://openalex.org/W24553703","https://openalex.org/W4211000692","https://openalex.org/W4212920271","https://openalex.org/W2612240612","https://openalex.org/W4211208250","https://openalex.org/W4211054902","https://openalex.org/W4324018414","https://openalex.org/W2170381940","https://openalex.org/W2472351724","https://openalex.org/W2993777277"],"abstract_inverted_index":{"MOTIVATION:":[0],"Taxonomic":[1],"analysis":[2],"of":[3,20,30,62,66,78,162,174,204,211],"environmental":[4,55],"microbial":[5,190,212],"communities":[6,22,213],"is":[7,58,223],"now":[8],"routinely":[9],"performed":[10,195],"thanks":[11],"to":[12,98,114,154,180,207],"advances":[13],"in":[14,23,53,159],"DNA":[15],"sequencing.":[16],"Determining":[17],"the":[18,28,60,111,175,197,202,205,209,232],"role":[19],"these":[21],"global":[24],"biogeochemical":[25,79,103,163,215],"cycles":[26,80],"requires":[27],"identification":[29],"their":[31,73],"metabolic":[32,67,100,160,166],"functions,":[33],"such":[34],"as":[35],"hydrogen":[36],"oxidation,":[37],"sulfur":[38],"reduction,":[39],"and":[40,72,185,192,231,242],"carbon":[41],"fixation.":[42],"These":[43],"functions":[44,68,101,167],"can":[45],"be":[46],"directly":[47],"inferred":[48],"from":[49,69,118,135],"metagenomics":[50],"data,":[51],"but":[52],"many":[54],"applications":[56],"metabarcoding":[57,70],"still":[59],"method":[61],"choice.":[63],"The":[64,137,165,199,220,227],"reconstruction":[65],"data":[71],"integration":[74],"into":[75],"coarse-grained":[76,172],"representations":[77],"remains":[81],"a":[82,90,106,127,144],"difficult":[83],"bioinformatics":[84],"problem":[85],"today.":[86],"RESULTS:":[87],"We":[88,177],"developed":[89,146],"pipeline,":[91],"called":[92],"Tabigecy,":[93],"which":[94],"exploits":[95],"taxonomic":[96],"affiliations":[97],"predict":[99,115],"constituting":[102],"cycles.":[104,164,176],"In":[105],"first":[107],"step,":[108],"Tabigecy":[109,179,221],"uses":[110],"tool":[112],"EsMeCaTa":[113,234],"consensus":[116,138],"proteomes":[117,139],"input":[119],"affiliations.":[120],"To":[121],"optimize":[122],"this":[123],"process,":[124],"we":[125],"generated":[126],"precomputed":[128,233],"database":[129,235],"containing":[130],"information":[131],"about":[132],"2404":[133],"taxa":[134],"UniProt.":[136],"are":[140,168,236],"searched":[141],"using":[142],"bigecyhmm,":[143],"newly":[145],"Python":[147,228],"package":[148,229],"relying":[149],"on":[150,171,196,214],"Hidden":[151],"Markov":[152],"Models":[153],"identify":[155],"key":[156],"enzymes":[157],"involved":[158],"function":[161],"then":[169],"projected":[170],"representation":[173],"applied":[178],"two":[181],"salt":[182],"cavern":[183],"datasets":[184],"validated":[186],"its":[187],"predictions":[188],"with":[189],"activity":[191],"hydrochemistry":[193],"measurements":[194],"samples.":[198],"results":[200],"highlight":[201],"utility":[203],"approach":[206],"investigate":[208],"impact":[210],"processes.":[216],"AVAILABILITY":[217],"AND":[218],"IMPLEMENTATION:":[219],"pipeline":[222],"available":[224,239],"at":[225,240],"https://github.com/ArnaudBelcour/tabigecy.":[226],"bigecyhmm":[230],"also":[237],"separately":[238],"https://github.com/ArnaudBelcour/bigecyhmm":[241],"https://doi.org/10.5281/zenodo.13354073,":[243],"respectively.":[244]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-06-20T22:02:38.213706","created_date":"2025-10-10T00:00:00"}
